[maker-devel] what is a 'model file' for the web annotation service?

[Steven Sullivan]

Sorry if this is a dumb question.

Using the MAKER web service I have the option of adding an AUGUSTUS 'model
file' as input

I generated a  training set of genes from my species through use of online
AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
sequences,and a set of protein sequences from those cDNAs, for the species.
I received these files (folders) back from the AUGUSTUS server (in addition
to log and err files):


*Species parameter archive*:  parameters.tar.gz

*Training genes: * training.gb.gz

*Ab initio predictions*:  ab_initio.tar.gz

*predictions with hints:*  hints_pred.tar.gz



The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
train itself. The format is Genbank.

the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
folders), 1 gff and 1 gtf.

Do you know which file would be correct for input to online MAKER as a
'model' file?


(NB there is no UTR predictions file, as my input cDNAs did not have enough
UTR information in them )
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